X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
Temperature 293.0
Details PEG 3350, sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 43.59 α = 90
b = 56.46 β = 90
c = 56.93 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2000-06-01
Diffraction Radiation
Monochromator Protocol
Si(111) double-crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 14-BM-D 1.0 APS 14-BM-D

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
1.64 25.4 97.1 0.036 -- -- 10.3 17258 17258 0.0 0.0 --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
1.64 1.71 86.0 0.2 -- 6.1 -- --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT, Structure of MLC1P bound to IQ 2 AND 3 (SOLVED BY MAD METHOD) 1.65 25.0 -- 0.0 16255 16255 869 98.0 -- 0.19284 0.19084 0.22788 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 1.65 1.693 1109 56 1109 0.229 0.275 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model overall anisotropic
Mean Isotropic B 24.235
Anisotropic B[1][1] 0.55
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.12
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.67
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.013
r_mcangle_it 1.816
r_scbond_it 2.864
r_nbd_refined 0.22
r_symmetry_vdw_refined 0.208
r_symmetry_hbond_refined 0.15
r_scangle_it 4.751
r_xyhbond_nbd_refined 0.159
r_angle_refined_deg 1.365
r_dihedral_angle_1_deg 3.089
r_chiral_restr 0.097
r_mcbond_it 1.009
r_dihedral_angle_3_deg 11.58
r_gen_planes_refined 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1379
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 252

Software

Software
Software Name Purpose
HKL-2000 data collection
SCALEPACK data scaling
AMoRE phasing
REFMAC refinement version: 5.0
HKL-2000 data reduction